BN1747 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.3129e-06 2.9029e-03
Layer 2 1.7272e-06 2.1798e-02
Layer 4 3.9189e-06 3.2867e-04
Layer 5 1.0596e-04 3.4034e-03
Layer 6 1.3498e-03 1.6209e-02
WM 6.1334e-02 1.6184e-01
Layer 1 6.1333e-01 5.2963e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
CHGA Expression Distribution
Gene Specificity Score (GSS)
CHGA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
CHGA Layer 4 2.5508 0.6642
SNCA Layer 5 2.2363 0.6586
SYNGR1 Layer 4 2.5566 0.6436
ANXA6 Layer 5 2.4053 0.6373
CAMK2G Layer 4 2.2168 0.6362
SH3GL2 Layer 4 2.3623 0.6361
UBE2V2 Layer 4 2.1807 0.6359
BEX5 Layer 4 2.3213 0.6351
GABARAPL1 Layer 5 2.1348 0.6350
MOAP1 Layer 4 2.2393 0.6350
NEUROD2 Layer 4 2.2695 0.6345
RNPS1 Layer 4 2.1484 0.6270
CEND1 Layer 4 2.4727 0.6259
PAFAH1B1 Layer 5 2.0859 0.6233
INPP5F Layer 4 2.3594 0.6223
EVL Layer 4 2.3750 0.6219
TCEAL2 Layer 4 2.2168 0.6204
SNAP91 Layer 4 2.4756 0.6190
GOT1 Layer 3 2.2422 0.6188
TUBA4A Layer 4 2.2773 0.6188
NCOA7 Layer 5 2.1055 0.6174
NELL2 Layer 4 2.4023 0.6168
APBA2 Layer 4 2.2695 0.6164
TOLLIP Layer 4 2.4023 0.6158
NUAK1 Layer 4 2.5664 0.6152
CD99L2 Layer 3 2.2070 0.6146
CLTA Layer 4 2.1221 0.6135
STX1B Layer 4 2.4238 0.6133
RPH3A Layer 4 2.3711 0.6129
OTUB1 Layer 4 2.3398 0.6128
NDUFA5 Layer 5 2.0723 0.6124
SNX10 Layer 3 2.4082 0.6115
AP2S1 Layer 5 2.1816 0.6112
CPLX1 Layer 4 2.3750 0.6107
PNMA8A Layer 4 2.3555 0.6106
CLSTN3 Layer 4 2.3105 0.6106
MAPK9 Layer 4 2.3154 0.6105
KCNA2 Layer 4 2.6777 0.6105
MAGED2 Layer 4 2.3818 0.6101
HARS Layer 4 2.1123 0.6087
SPOCK2 Layer 4 2.1699 0.6083
NDUFS2 Layer 4 2.2490 0.6082
TTC9B Layer 4 2.7070 0.6081
ADAM23 Layer 3 2.1387 0.6076
NAPA Layer 4 2.1973 0.6065
TUBB3 Layer 4 2.3926 0.6063
PNKD Layer 4 2.1055 0.6052
SYNJ1 Layer 5 2.2373 0.6051
ACTR1A Layer 4 1.9697 0.6037
HERC1 Layer 4 2.3311 0.6034

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1747
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1747_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1747/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1747/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1747/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1747/report/PD/BN1747_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1747/report/PD/BN1747_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 06:36:57
  • Number of Processes: 10
  • Spending Time: 0h 5m